Hi Alan, Hmm...you need to use "nt_arg" and "ct_glu" fragment names. Otherwise, you won't get the C-terminal oxygen.
Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 USA . Biz:(650)-872-0942 Tech:(650)-872-0834 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:war...@delsci.com > -----Original Message----- > From: pymol-users-ad...@lists.sourceforge.net > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Alan > Sent: Monday, March 20, 2006 12:16 PM > To: Warren DeLano > Cc: Pymol > Subject: Re: [PyMOL] Saving PDB with CONECT information > > Thanks a lot Warren. > > If you allow me, my script to build sequences of 3 peptides > is almost done. I could even use sculpt to improve my > molecules structures. > > For the moment I am missing just one thing. I want to make > the N-term and C-term (NH3+ and COO-) automatically for all > 20 tripeptide. I know how to to do it by mouse, but how to > 'add hydrogens' and 'make pk1 positive', e. g., by command? > > Thanks a lot for PyMol. > > Cheers, > Alan > > On 20/03/06, Warren DeLano <war...@delsci.com> wrote: > > Alan, > > > > > Is PyMol able to save the built protein/molecule in a PDB > file with > > > CONECT information. If so, how to do it? > > > > Yes, > > > > set pdb_conect_all > > > > before saving the pdb file in order to get a PDB file with explicit > > connectivity and valences for all atoms. > > > > Cheers, > > Warren > > > > -- > > Warren L. DeLano, Ph.D. > > Principal Scientist > > > > . DeLano Scientific LLC > > . 400 Oyster Point Blvd., Suite 213 > > . South San Francisco, CA 94080 USA > > . Biz:(650)-872-0942 Tech:(650)-872-0834 . Fax:(650)-872-0273 > > Cell:(650)-346-1154 . mailto:war...@delsci.com > > > > > > > -----Original Message----- > > > From: pymol-users-ad...@lists.sourceforge.net > > > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Alan > > > Sent: Monday, March 20, 2006 11:39 AM > > > To: Pymol > > > Subject: [PyMOL] Saving PDB with CONECT information > > > > > > Hello List! > > > > > > Is PyMol able to save the built protein/molecule in a PDB > file with > > > CONECT information. If so, how to do it? > > > > > > Thanks in advance for any help. > > > > > > Cheers, > > > Alan > > > -- > > > Alan Wilter S. da Silva, D.Sc. - Research Associate Department of > > > Biochemistry, University of Cambridge. > > > 80 Tennis Court Road, Cambridge CB2 1GA, UK. > > > > > > > > > ------------------------------------------------------- > > > This SF.Net email is sponsored by xPML, a groundbreaking > scripting > > > language that extends applications into web and mobile > media. Attend > > > the live webcast and join the prime developer group breaking into > > > this new coding territory! > > > http://sel.as-us.falkag.net/sel?cmd=k&kid0944&bid$1720&dat1642 > > > _______________________________________________ > > > PyMOL-users mailing list > > > PyMOL-users@lists.sourceforge.net > > > https://lists.sourceforge.net/lists/listinfo/pymol-users > > > > > > > > > > > > > > > > > -- > Alan Wilter S. da Silva, D.Sc. - Research Associate > Department of Biochemistry, University of Cambridge. > 80 Tennis Court Road, Cambridge CB2 1GA, UK. > > > ------------------------------------------------------- > This SF.Net email is sponsored by xPML, a groundbreaking > scripting language that extends applications into web and > mobile media. Attend the live webcast and join the prime > developer group breaking into this new coding territory! > http://sel.as-us.falkag.net/sel?cmd=k&kid0944&bid$1720&dat1642 > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users > > > >
